ReferenceMapper: QC checks

[Nigel]

Hi,

I have captured and sequenced a 5Mb region which contained about 115 genes

For a publication I need to establish some not so obvious QC criteria. I need to work out how many exons were covered by the capture and 454 sequencing and if there are any exons that weren’t sequenced.

Also I need to figure out how many SNPs in total were reported in the HCDiffs table and the known SNPs that were called, what are their allele frequencies.

Any tips.......

Many thanks,
N